This is a difficult problem, I believe. I asked Indic-script expert Apurva Ashar, and he replied:
Yes, this is something on which I have done extensive work. I thinks InDesign can be a great life-changer for jobs like this. I have number of scripts (basically its is multiple search-replace—combination of some text and some GREP searches executed in batch) ready for the purpose.
The basic problem is: we in India have been using non-Unicode/non-standard fonts for Indic publishing till now. Indic character Glyphs were placed on normal English fonts and keyboard mapper software were used for data input. There are several hundred variations in these fonts and they does not exist any standard. I am attaching two small videos, though the commentary is in Gujarati, you will understand most of it by the visuals. This script works for mixed languages, mixed fonts etc.
This in fact is the biggest problem/opportunity in Indic publishing. at this moment of time in India. Lot of old data in various proprietary fonts and in Pagemaker to be converted to Unicode and InDesign, keeping formatting intact. There are also problems of Unicode fonts, InDesign training, eBooks in Indic fonts…